Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
|---|
| natural killer t cells recognize diacylglycerol antigens from pathogenic bacteria. | natural killer t (nkt) cells recognize glycosphingolipids presented by cd1d molecules and have been linked to defense against microbial infections. previously defined foreign glycosphingolipids recognized by nkt cells are uniquely found in nonpathogenic sphingomonas bacteria. here we show that mouse and human nkt cells also recognized glycolipids, specifically a diacylglycerol, from borrelia burgdorferi, which causes lyme disease. the b. burgdorferi-derived, glycolipid-induced nkt cell prolifera ... | 2006 | 16921381 |
| genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. | to investigate the diversity of dioxygenase genes involved in polycyclic aromatic hydrocarbon (pah)-degradation, a total of 32 bacterial strains were isolated from surface mangrove sediments, from the genera mycobacterium, sphingomonas, terrabacter, sphingopyxis, sphingobium and rhodococcus. two sets of pcr primers were constructed to detect the nida-like and nahac-like sequences of the alpha subunit of the pah ring-hydroxylating dioxygenase. pcr amplified the dna fragments from all gram-positiv ... | 2006 | 16923069 |
| cloning, expression, purification, crystallization and preliminary structure determination of glucose-1-phosphate uridylyltransferase (ugpg) from sphingomonas elodea atcc 31461 bound to glucose-1-phosphate. | the cloning, expression, purification, crystallization and preliminary crystallographic analysis of glucose-1-phosphate uridylyltransferase (ugpg) from sphingomonas elodea atcc 31461 bound to glucose-1-phosphate are reported. diffraction data sets were obtained from seven crystal forms in five different space groups, with highest resolutions ranging from 4.20 to 2.65 a. the phase problem was solved for a p2(1) crystal form using multiple isomorphous replacement with anomalous scattering from an ... | 2006 | 16946483 |
| cutting edge: impaired glycosphingolipid trafficking and nkt cell development in mice lacking niemann-pick type c1 protein. | niemann-pick type c1 (npc1) is a late endosomal/lysosomal transmembrane protein involved in the cellular transport of glycosphingolipids and cholesterol that is mutated in a majority of patients with niemann-pick c neurodegenerative disease. we found that npc1-deficient mice lacked valpha14-jalpha18 nkt cells, a major population of cd1d-restricted t cells that is conserved in humans. npc1-deficient mice also exhibited marked defects in the presentation of sphingomonas cell wall ags to nkt cells ... | 2006 | 16785493 |
| caver: a new tool to explore routes from protein clefts, pockets and cavities. | the main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. | 2006 | 16792811 |
| gram-negative bacteria from patients seeking medical advice in stockholm after the tsunami catastrophe. | microbiological cultures from 229 patients seeking medical advice in stockholm after the tsunami catastrophe of december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative bacilli were the most common findings from wound cultures. common human pathogens such as escherichia coli, proteus species, klebsiella spp., and pseudomonas aeruginosa were isolated. more rare species of gram-negative bacilli, e.g. myroides odoratus, sp ... | 2006 | 16798691 |
| identification and functional analysis of the genes for naphthalenesulfonate catabolism by sphingomonas xenophaga bn6. | sphingomonas xenophaga bn6 degrades various (substituted) naphthalenesulfonates to the corresponding (substituted) salicylates. a gene cluster was identified on the plasmid pbn6 which coded for several enzymes participating in the degradative pathway for naphthalenesulfonates. a dna fragment of 16 915 bp was sequenced which contained 17 orfs. the genes encoding the 1,2-dihydroxynaphthalene dioxygenase, 2-hydroxychromene-2-carboxylate isomerase, and 2'-hydroxybenzalpyruvate aldolase of the naphth ... | 2006 | 16804169 |
| cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from sphingomonas sp. strain 113p3, a novel-type quinohaemoprotein alcohol dehydrogenase. | a gene for periplasmic poly(vinyl alcohol) (pva) dehydrogenase (pvadh) was cloned, based on the n-terminal amino acid sequence of the purified pvadh from sphingomonas sp. 113p3 and the sequence of the gene for pvadh (pvaa, genbank accession no. ab190288). the recombinant pvadh tagged with hexahistidine was expressed in escherichia coli and purified to homogeneity. the recombinant enzyme had the same characteristics as the purified enzyme from sphingomonas sp. strain 113p. in addition to pva, the ... | 2006 | 16804170 |
| bacterial community in ancient siberian permafrost as characterized by culture and culture-independent methods. | the microbial composition of ancient permafrost sediments from the kolyma lowland of northeast eurasia was examined through culture and culture-independent approaches. these sediments have been continuously frozen for 5,000 to 2-3 million years. a total of 265 bacteria 16s rrna gene sequences were amplified from the permafrost total-community genomic dna and screened by amplified ribosomal 16s rrna restriction analysis. members of three major lineages were found: gamma-proteobacteria (mostly xan ... | 2006 | 16805696 |
| characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in guanabara bay, brazil. | hydrocarbonoclastic bacterial communities inhabiting mangrove sediments were characterized by combining molecular and culture-dependent approaches. surface sediments were collected at two sampling sites in guanabara bay (rio de janeiro, brazil) and used to inoculate in vitro enrichment cultures containing crude oil to obtain hydrocarbonoclastic bacterial consortia. in parallel, in situ mesocosms (located in the guapimirim mangrove) were contaminated with petroleum. comparison of bacterial commun ... | 2006 | 16815684 |
| purification and characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols. | initial reactions involved in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs) include a ring-dihydroxylation catalyzed by a dioxygenase and a subsequent oxidation of the dihydrodiol products by a dehydrogenase. in this study, the dihydrodiol dehydrogenase from the pah-degrading sphingomonas strain chy-1 has been characterized. the bphb gene encoding pah dihydrodiol dehydrogenase (pddh) was cloned and overexpressed as a his-tagged protein. the recombinant protein was purified ... | 2006 | 16820465 |
| purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, rdpa and sdpa, from sphingomonas herbicidovorans mh. | alpha-ketoglutarate-dependent (r)-dichlorprop dioxygenase (rdpa) and alpha-ketoglutarate-dependent (s)-dichlorprop dioxygenase (sdpa), which are involved in the degradation of phenoxyalkanoic acid herbicides in sphingomonas herbicidovorans mh, were expressed and purified as his6-tagged fusion proteins from escherichia coli bl21(de3)(plyss). rdpa and sdpa belong to subgroup ii of the alpha-ketoglutarate-dependent dioxygenases and share the specific motif hxdx(24)tx(131)hx(10)r. amino acids his-11 ... | 2006 | 16820480 |
| improvement in production and quality of gellan gum by sphingomonas paucimobilis under high dissolved oxygen tension levels. | the effect of agitation rate and dissolved oxygen tension (dot) on growth and gellan production by sphingomonas paucimobilis was studied. higher cell growth of 5.4 g l(-1) was obtained at 700 rpm but maximum gellan (15 g l(-1)) was produced at 500 rpm. dot levels above 20% had no effect on cell growth but gellan yield was increased to 23 g l(-1 )with increase in dot level to 100%. higher dot levels improved the viscosity and molecular weight of the polymer with change in acetate and glycerate co ... | 2006 | 16820976 |
| characterization of four rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols. | four genes were isolated and characterized for alcohol dehydrogenases (adhs) catalyzing the oxidation of aromatic alcohols such as benzyl alcohol to their corresponding aldehydes, one from o-xylene-degrading rhodococcus opacus tkn14 and the other three from n-alkane-degrading rhodococcus erythropolis pr4. various aromatic alcohols were bioconverted to their corresponding carboxylic acids using escherichia coli cells expressing each of the four adh genes together with an aromatic aldehyde dehydro ... | 2006 | 16292529 |
| characterization of the novel hch-degrading strain, microbacterium sp. itrc1. | a gram-positive microbacterium sp. strain, itrc1, that was able to degrade the persistent and toxic hexachlorocyclohexane (hch) isomers was isolated and characterized. the itrc1 strain has the capacity to degrade all four major isomers of hch present in both liquid cultures and aged contaminated soil. dna fragments corresponding to the two initial genes involved in gamma-hch degradative pathway, encoding enzymes for gamma-pentachlorocyclohexene hydrolytic dehalogenase (linb) and a 2,5-dichloro-2 ... | 2006 | 16315057 |
| efficient production of 2-pyrone 4,6-dicarboxylic acid as a novel polymer-based material from protocatechuate by microbial function. | sphingomonas paucimobilis syk-6, which can degrade various low molecular weight compounds derived from plant polyphenols such as lignin, lignan, and tannin, metabolizes these substances via 2-pyrone-4,6-dicarboxylic acid (pdc). we focused on this metabolic intermediate as a potential raw material for novel, bio-based polymers. we cloned the ligab and ligc genes of syk-6, which respectively encode protocatechuate 4,5-dioxygenase and 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase, into a ... | 2006 | 16322989 |
| survey of environmental biocontamination on board the international space station. | the international space station (iss) is an orbital living and working environment extending from the original zarya control module built in 1998. the expected life span of the completed station is around 10 years and during this period it will be constantly manned. it is inevitable that the iss will also be home to an unknown number of microorganisms. this survey reports on microbiological contamination in potable water, air, and on surfaces inside the iss. the viable counts in potable water di ... | 2006 | 16364606 |
| influence of growth phase on the phospholipidic fatty acid composition of two marine bacterial strains in pure and mixed cultures. | this in vitro study was conducted in order to determine the effects of hydrocarbons and growth phase on the phospholipid ester-linked fatty acid composition of two marine sedimentary hydrocarbon-degrading bacteria. these two strains, namely corynebacterium sp. and sphingomonas sp. 2mpii, were cultivated on either a simple soluble substrate (ammonium acetate) or a hydrocarbon (respectively n-eicosane and phenanthrene). the incubations were stopped at different times corresponding to point of lag ... | 2006 | 16380233 |
| biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p- dioxin by sphingomonas wittichii strain rw1. | sphingomonas wittichii rw1 is able to catabolize 1,2,3,4-tetrachlorodibenzo-p-dioxin (h. b. hong, y. s. chang, i. h. nam, p. fortnagel, and s. schmidt, appl. environ. microbiol. 68:2584-2588, 2002). here we demonstrate the aerobic bacterial catabolism of the ubiquitous toxic diaryl ether pollutant 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by this strain. the products of this biotransformation were identified as tetrachlorocatechol and 2-methoxy-3,4,5,6-tetrachlorophenol by comparing mass spectra re ... | 2006 | 16391032 |
| slow-release inoculation allows sustained biodegradation of gamma-hexachlorocyclohexane. | this study investigated the feasibility of a slow-release inoculation approach as a bioaugmentation strategy for the degradation of lindane (gamma-hexachlorocyclohexane [gamma-hch]). slow-release inoculation of sphingomonas sp. gamma 1-7 was established in both liquid and soil slurry microcosms using open-ended silicone tubes in which the bacteria are encapsulated in a protective nutrient-rich matrix. the capacity of the encapsulated cells to degrade lindane under aerobic conditions was evaluate ... | 2006 | 16391099 |
| distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from spain. | hexachlorocyclohexane (hch)-degrading bacteria are believed to mediate natural attenuation of hch contamination and have potential for active bioremediation processes. this study addressed the very limited understanding of the distribution, diversity and substrate specificity of such bacteria from 13 soil samples, varying in levels of hch contamination, from four sites in spain. hexachlorocyclohexane removal occurred in 16 of 36 enrichment cultures. hexachlorocyclohexane-degrading populations we ... | 2006 | 16343322 |
| composition of microbial communities in hexachlorocyclohexane (hch) contaminated soils from spain revealed with a habitat-specific microarray. | microarray technology was used to characterize and compare hexachlorocyclohexane (hch) contaminated soils from spain. a library of 2,290 hypervariable 16s rrna gene sequences was prepared with serial analysis of ribosomal sequence tags (sarst) from a composite of contaminated and uncontaminated soils. by designing hybridization probes specific to the 100 most abundant ribosomal sequence tags (rsts) in the composite library, the rst array was designed to be habitat-specific and predicted to monit ... | 2006 | 16343328 |
| isolation and physiological characterization of the pentachlorophenol degrading bacterium sphingomonas chlorophenolica. | many chlorophenols tend to persist in the environment, and they may become public health hazards. among chlorophenols, pentachlorophenol (pcp) is a priority pollutant that has been used widely as a general biocide in commercial wood treatment. owing to the rapid industrial growth, serious soil and water pollutions by chlorophenols has been reported in taiwan. in this study, 10 indigenous pcp-degrading bacterial strains were isolated from a pcp-degrading mixed culture, and the potential of both t ... | 2006 | 16005492 |
| the degradation of alpha-quaternary nonylphenol isomers by sphingomonas sp. strain ttnp3 involves a type ii ipso-substitution mechanism. | the degradation of radiolabeled 4(3',5'-dimethyl-3'-heptyl)-phenol [nonylphenol (np)] was tested with resting cells of sphingomonas sp. strain ttnp3. concomitantly to the degradation of np, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. two other radiolabeled isomers of np, 4(2',6'-dimethyl-2'-heptyl)-phenol and 4(3',6'-dimethyl-3'-heptyl)-phenol, were synthesized. in parallel experiments, the 4(2', ... | 2006 | 16091931 |
| expression of glycosylated haloalkane dehalogenase linb in pichia pastoris. | heterologous expression of the bacterial enzyme haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 in methylotrophic yeast pichia pastoris is reported. the haloalkane dehalogenase gene linb was subcloned into the ppiczalphaa vector and integrated into the genome of p. pastoris. the recombinant linb secreted from the yeast was purified to homogeneity and biochemically characterized. the deglycosylation experiment and mass spectrometry measurements showed that the recombinant linb ex ... | 2006 | 16216524 |
| degradability of dimethyl terephthalate by variovorax paradoxus t4 and sphingomonas yanoikuyae dos01 isolated from deep-ocean sediments. | two strains of bacteria were isolated from deep-ocean sediments of the south china sea using enrichment culturing technique and they were identified as sphingomonas yanoikuyae dos01 (ay878409) and variovorax paradoxus t4 (ay878410) based on 16s rrna gene sequences. s. yanoikuyae dos01 was only capable of transforming dimethyl terephthalate (dmtp) to monomethyl terephthalate (mmtp) without further degradation while v. paradoxus t4 exhibited ability in mineralizing dmtp as the sole source of carbo ... | 2006 | 16955363 |
| description of sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of sphingomonas cloacae as sphingobium cloacae comb. nov. | a phenanthrene-degrading bacterium, strain tkp(t), was isolated from a fly ash dumping site of the thermal power plant in panki, kanpur, india, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. phylogenetic analysis based on 16s rrna gene sequences indicated that the strain belonged to the genus sphingobium, as it showed highest sequence similarity to sphingobium herbicidovorans dsm 11019(t) (97.3 %) and sphingomonas cloacae jcm 10874(t) (96.5 %), compar ... | 2006 | 16957112 |
| sphingomonas dokdonensis sp. nov., isolated from soil. | a gram-negative, rod-shaped, sphingomonas-like bacterial strain, ds-4(t), was isolated from soil of dokdo, korea, and its taxonomic position was investigated using a polyphasic approach. strain ds-4(t) grew optimally on trypticase soy agar medium without nacl at ph 6.0-6.5 and 25 degrees c. it contained q-10 as the predominant ubiquinone and c(18 : 1)omega7c, c(16 : 0), c(14 : 0) 2-oh and c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh as the major fatty acids. sphingoglycolipid, phosphatidylcholine, ... | 2006 | 16957115 |
| identification and quantification of uncultivated proteobacteria associated with pyrene degradation in a bioreactor treating pah-contaminated soil. | uncultivated bacteria associated with the degradation of pyrene in a bioreactor treating soil contaminated with polycyclic aromatic hydrocarbons (pah) were identified by dna-based stable-isotope probing (sip) and quantified by real-time quantitative pcr. most of the 16s rrna gene sequences recovered from (13)c-enriched dna fractions clustered phylogenetically within three separate groups of beta- and gamma-proteobacteria unassociated with described genera and were designated "pyrene groups 1, 2 ... | 2006 | 16958754 |
| novel upper meta-pathway extradiol dioxygenase gene diversity in polluted soil. | for the determination of the catabolic community diversity that is related to biodegradation potential, we developed a protocol for the assessment of catabolic marker genes in polluted soils. primers specific to upper pathway extradiol dioxygenase genes were designed which amplified a 469-bp product from sphingomonas sp. hv3. the constructed primers were used in pcr amplification of upper pathway ring cleavage genes from dna directly isolated from a mineral oil polluted landfill site, a mineral ... | 2006 | 16958914 |
| linear 3-hydroxybutyrate tetramer (hb4) produced by sphingomonas sp. is characterized as a growth promoting factor for some rhizomicrofloral composers. | sphingomonas spp. of alpha-proteobacteria often play a role in assisting the development of microfloral communities under adverse soil conditions. using a frateuria sp. as an indicator for bacterial growth assay, we investigated the bacterial growth-promoting factor in the culture fluids of sphingomonas sp. ec-k085. this factor was successfully isolated and identified as linear (r,r,r,r)-3-hydroxybutyrate tetramer (hb4), having a hydroxy-end and a carboxy-end group. when 28 mug of hb4 was charge ... | 2006 | 16960351 |
| microbial degradation of nonylphenol and other alkylphenols--our evolving view. | because the endocrine disrupting effects of nonylphenol (np) and octylphenol became evident, the degradation of long-chain alkylphenols (ap) by microorganisms was intensively studied. most np-degrading bacteria belong to the sphingomonads and closely related genera, while np metabolism is not restricted to defined fungal taxa. growth on np and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. while both bacterial and fungal d ... | 2006 | 16826376 |
| multisubstrate biodegradation kinetics for binary and complex mixtures of polycyclic aromatic hydrocarbons. | biodegradation kinetics were studied for binary and complex mixtures of nine polycyclic aromatic hydrocarbons (pahs): naphthalene, 1-methylnaphthalene, 2-methylnaphthalene, 2-ethylnaphthalene, phenanthrene, anthracene, pyrene, fluorene, and fluoranthene. discrepancies between the observed biodegradation rates and those predicted by a sole-substrate model indicate that significant substrate interactions occurred in both the binary and complex-mixture experiments. for all compounds except naphthal ... | 2006 | 16833134 |
| removal and biodegradation of polycyclic aromatic hydrocarbons by selenastrum capricornutum. | the removal and degradation of a mixture of polycyclic aromatic hydrocarbons (pahs), namely phenanthrene (phe), fluoranthene (fla), and pyrene (pyr), by a green microalgal species, selenastrum capricornutum, at different initial cell densities were studied. the pah removal efficiency increased with the initial cell density, and 96% of phe, 100% of fla, and 100% of pyr in the medium were removed by live s. capricornutum at the density of 1 x 10(7) cells/ml in 4 d, whereas less than 50% of pahs we ... | 2006 | 16833137 |
| bacterial decontamination of duwl biofilm using oxygenal 6. | the aim of this study was bacteriological assessment of the dental unit waterlines (duwl) biofilm - concentration and composition of the aerobe and facultative anaerobe bacterial microflora, and evaluation of the influence of a disinfecting product, oxygenal 6, on the biofilm composition. tubing fragments were taken from 25 units twice, before and after disinfection, and bacterial suspension of the biofilm was obtained from the samples. the bacterial flora was determined with the plate culture m ... | 2006 | 16841887 |
| functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from sphingomonas sp. strain a4. | sphingomonas sp. strain a4 is capable of utilizing acenaphthene as its sole carbon and energy source. to isolate the genes responsible for acenaphthene degradation, transposon mutagenesis was performed on strain a4 and four mini-tn5-inserted mutants lacking the ability to utilize acenaphthene were isolated. in three of the four mini-tn5 inserted mutants, the mini-tn5s were inserted into the same locus (within about 16 kb) as the arha1a2 genes, which had previously been identified as the genes en ... | 2006 | 16849808 |
| postoperative endophthalmitis caused by sphingomonas paucimobilis. | we present a case in which a new organism, sphingomonas paucimobilis, caused endophthalmitis after phacoemulsification in a 73-year-old woman. the case shows a recurrent acute endophthalmitis with complete resolution only after vitrectomy. this organism has not been described as a cause of endophthalmitis and was resistant to initial medical management. we also describe an interaction between this organism and a co-infective organism that may account for the unusual clinical course. | 2006 | 16857516 |
| characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons. | in sphingomonas chy-1, a single ring-hydroxylating dioxygenase is responsible for the initial attack of a range of polycyclic aromatic hydrocarbons (pahs) composed of up to five rings. the components of this enzyme were separately purified and characterized. the oxygenase component (ht-phni) was shown to contain one rieske-type [2fe-2s] cluster and one mononuclear fe center per alpha subunit, based on epr measurements and iron assay. steady-state kinetic measurements revealed that the enzyme had ... | 2006 | 17014090 |
| blooms of single bacterial species in a coastal lagoon of the southwestern atlantic ocean. | we investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern atlantic ocean. alphaproteobacteria formed the dominant microbial group in both zones throughout the sampling period. after an intrusion of marine water, members of the sar11 lineage became abundant in the brackish-water zone. these bacteria were apparently distributed ove ... | 2006 | 17021206 |
| [construction of double-labelled carbofuran-degrading bacterium sphingomonas sp. cds-1]. | the genomic dna of a carbofuran-degrading bacterium sphingomonas sp. cds-1 was digested by sau3al and ligated to probe-gfp digested by bamhi, and the product was transformed to the e. coli dh5alpha competent cells. fifty positive clones that could emit green fluorescence under uv were selected from about 1 x 10(4) clones grown on selective plates amplb. one clone f7 with the strongest fluorescence was selected, the recombinant plasmid pf7 from this clone was digested with ecor i & hind iii and t ... | 2006 | 17037065 |
| removal of cyanobacteria, cyanotoxins, heterotrophic bacteria and endotoxins at an operating surface water treatment plant. | the removal of cyanobacteria, hepatotoxins produced by them (microcystins), phytoplankton, heterotrophic bacteria and endotoxins were monitored at a surface water treatment plant with coagulation, clarification, sand filtration, ozonation, slow sand filtration and chlorination as the treatment process. coagulation-sand filtration reduced microcystins by 1.2-2.4, and endotoxins by 0.72-2.01 log10 units. ozonation effectively removed the residual microcystins. the treatment process reduced phytopl ... | 2006 | 17037128 |
| statistical approach to optimization of fermentative production of gellan gum from sphingomonas paucimobilis atcc 31461. | gellan gum, a high-molecular-weight anionic linear polysaccharide produced by pure-culture fermentation from sphingomonas paucimobilis atcc 31461, has elicited industrial interest in recent years as a high-viscosity biogum, a suspending agent, a gelling agent, and an agar substitute in microbial media. in this paper we report on the optimization of gellan gum production using a statistical approach. in the first step, the one factor-at-a-time method was used to investigate the effect of medium c ... | 2006 | 17046526 |
| directed evolution of a non-heme-iron-dependent extradiol catechol dioxygenase: identification of mutants with intradiol oxidative cleavage activity. | the non-heme-iron(ii)-dependent extradiol catechol dioxygenases catalyse the oxidative cleavage of substituted catechols found on bacterial aromatic degradation pathways. the reaction mechanism of the extradiol dioxygenases is believed to proceed through the same proximal hydroperoxide intermediate as the iron(iii)-dependent intradiol catechol dioxygenases. directed evolution was carried out on members of the class iii extradiol catechol dioxygenases, by using 1) error-prone polymerase chain rea ... | 2006 | 17051653 |
| bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils. | soils contaminated with mineral oil hydrocarbons are often cleaned in off-site bioremediation systems. in order to find out which bacteria are active during the degradation phase in such systems, the diversity of the active microflora in a degrading soil remediation system was investigated by small-subunit (ssu) rrna analysis. two sequential rna extracts from one soil sample were generated by a procedure incorporating bead beating. both extracts were analysed separately by generating individual ... | 2006 | 17074900 |
| [analysis of the degrading products of carbofuran by sphingomonas sp. with gc/ms and gc/ftir]. | in different degrading phases, the degrading products of carbofuran by cds-1(sphingomonas sp. ) were extracted by acetone. according to the analysis of gas chromatography/mass spectrometry (gc/ms), carbofuran-7-phenol was identified as the initial degrading product, and an unknown metabolite with molecular weight of 182 was determined as 2-hydroxyl-3-tertiarybutylalcohol-phenol, which was the next degrading product of carbofuran-7-phenol. according to the analysis of gc/ms and gas chromatography ... | 2006 | 17112053 |
| characterization of alkylphenol degradation gene cluster in pseudomonas putida mt4 and evidence of oxidation of alkylphenols and alkylcatechols with medium-length alkyl chain. | alkylphenols (aps) are ubiquitous contaminants in aquatic environments and have endocrine disrupting and toxic effects on aquatic organisms. to investigate biodegradation mechanisms of aps, an ap degradation gene cluster was cloned from a butylphenol (bp)-degrading bacterium, pseudomonas putida mt4. the gene cluster consisted of 13 genes named bupba1a2a3a4a5a6cehifg. from the nucleotide sequences, bupa1a2a3a4a5a6 were predicted to encode a multicomponent phenol hydroxylase (ph), whereas bupbcehi ... | 2006 | 17116584 |
| molecular diversity studies of bacterial communities of oil polluted microbial mats from the etang de berre (france). | the biodiversity of microbial mats inhabiting the oil-contaminated lagoon etang de berre was determined by molecular approaches. the fingerprint of denaturing gradient gel electrophoresis (dgge) and automatic ribosomal intergenic spacer analysis (arisa) of mats exposed to different pollution levels showed specific microbial communities for each site but similar diversity richness. species composition of the mats were compared by constructing 16s rrna libraries. amplified rdna restriction analysi ... | 2006 | 17117996 |
| [isolation, identification and characteristics of a fenpropathrin-degrading bacterium jql4-5]. | a bacterium capable of utilizing fenpropathrin as sole carbon source was isolated from activated sludge collected from wastewater treating system of a pesticide manufacturer. this bacterium was identified as sphingomonas sp. according to its physiological & biochemical analysis and the similarity analysis of its 16s rdna sequence (genbank accession no. dq177525). this bacterium could degrade 99.8% of 20 mg/l fenpropathrin in 24h. the optimal ph and temperature for the degradation were 7.0 and 30 ... | 2006 | 17256618 |
| [presence of the microbiological risk in umbrian sawmills]. | the purpose of this study was to quantify and identify the airborne microbial contamination in umbria sawmills. in this paper we reported the preliminary results of our analysis. microbial contaminants (fungi and bacteria) were assessed with passive (ima standard) and active (sas microbial sampler) methods. there were significant differences of bacterial and/or fungal cfu/m3 values between the outdoor and indoor environments during the normal sawmills activity. staphylococcus, sphingomonas, past ... | 2006 | 17380948 |
| characterization of estrogen-degrading bacteria isolated from an artificial sandy aquifer with ultrafiltered secondary effluent as the medium. | this study investigated the aerobic and anoxic biodegradation of four estrogens [estrone (e1), estradiol (e2), estriol (e3), and the synthetic 17 alpha-ethinylestradiol (ee2)] in microcosms constructed with marine sand and ulftrafiltered (uf) secondary effluent. three estrogen-degrading bacteria, lhj1, lhj3, and cyh, were isolated. based on gram-stain morphology and 16s rrna sequence homology, lhj1 and lhj3 belong to the genus acinetobacter and agromyces, respectively; cyh matched to 95% with th ... | 2007 | 17396255 |
| characterization of a c-c bond hydrolase from sphingomonas wittichii rw1 with novel specificities towards polychlorinated biphenyl metabolites. | sphingomonas wittichii rw1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. we used inverse pcr to amplify dxnb2, a gene encoding one of three meta-cleavage product (mcp) hydrolases identified in the organism that are homologues of bphd involved in biphenyl catabolism. purified dxnb2 catalyzed the hydrolysis of 8-oh 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (hopda) approximately six times faster than for hopda at saturating substrate concentrations. moreover, the speci ... | 2007 | 17416660 |
| limits of propidium iodide as a cell viability indicator for environmental bacteria. | viability measurements of individual bacteria are applied in various scopes of research and industry using approaches where propidium iodide (pi) serves as dead cell indicator. the reliability of pi uptake as a cell viability indicator for dead (pi permeable) and viable (pi impermeable) bacteria was tested using two soil bacteria, the gram(-) sphingomonas sp. lb126 and the gram(+) mycobacterium frederiksbergense lb501t. | 2007 | 17421025 |
| endogenous sphingolipid metabolites related to the growth in sphingomonas chungbukensis. | sphingolipids are present in animals, plants, fungi, yeasts and some bacteria. in mammalian cells sphingolipids act as lipid mediators for cell growth, differentiation, apoptosis and angiogenesis. in contrast, in bacteria the biological significance of sphingolipids has not been fully elucidated and sphingolipid metabolism has not been investigated. the aim of this study was to compare the pattern of sphingolipid metabolites in hit-t15 beta cells originating from hamster pancreas to that in the ... | 2007 | 17424937 |
| the complex of sphingomonas elodea atcc 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members. | gellan gum is a widely used commercial material, available in many different forms. its economic importance has led to studies into the biosynthesis of exopolysaccharide gellan gum, which is industrially prepared in high yields using sphingomonas elodea atcc 31461. glucose-1-phosphate uridylyltransferase mediates the reversible conversion of glucose-1-phosphate and utp into udp-glucose and pyrophosphate, which is a key step in the biosynthetic pathway of gellan gums. here we present the x-ray cr ... | 2007 | 17434970 |
| potential of the adhesion of bacteria isolated from drinking water to materials. | heterotrophic bacteria (11 genera, 14 species, 25 putative strains) were isolated from drinking water, identified either biochemically or by partial 16s rdna gene sequencing and their adherence characteristics were determined by two methods: i. thermodynamic prediction of adhesion potential by measuring hydrophobicity (contact angle measurements) and ii. by measuring adherence to eight different substrata (asi 304 and 316 stainless steel, copper, polyvinyl chloride, polypropylene, polyethylene, ... | 2007 | 17440920 |
| the crystal structure of the ring-hydroxylating dioxygenase from sphingomonas chy-1. | the ring-hydroxylating dioxygenase (rhd) from sphingomonas chy-1 is remarkable due to its ability to initiate the oxidation of a wide range of polycyclic aromatic hydrocarbons (pahs), including pahs containing four- and five-fused rings, known pollutants for their toxic nature. although the terminal oxygenase from chy-1 exhibits limited sequence similarity with well characterized rhds from the naphthalene dioxygenase family, the crystal structure determined to 1.85 a by molecular replacement rev ... | 2007 | 17451434 |
| cell surface structure enhancing uptake of polyvinyl alcohol (pva) is induced by pva in the pva-utilizing sphingopyxis sp. strain 113p3. | polyvinyl alcohol (pva)-utilizing sphingopyxis sp. 113p3 (re-identified from sphingomonas sp. 113p3) removed almost 0.5% pva from culture supernatants in 4 days. faster degradation of 0.5% pva was performed by the periplasmic fraction. the average molecular size of pva in the culture supernatant or cell-bound pva was gradually shifted higher, suggesting that lower molecular size molecules are degraded faster. depolymerized products were found in neither the culture supernatant nor the cell-bound ... | 2007 | 17453173 |
| identification of an il-17-producing nk1.1(neg) inkt cell population involved in airway neutrophilia. | invariant natural killer t (inkt) cells are an important source of both t helper type 1 (th1) and th2 cytokines, through which they can exert beneficial, as well as deleterious, effects in a variety of inflammatory diseases. this functional heterogeneity raises the question of how far phenotypically distinct subpopulations are responsible for such contrasting activities. in this study, we identify a particular set of inkt cells that lack the nk1.1 marker (nk1.1(neg)) and secrete high amounts of ... | 2007 | 17470641 |
| sphingomonas mucosissima sp. nov. and sphingomonas desiccabilis sp. nov., from biological soil crusts in the colorado plateau, usa. | two bacterial strains, cp173-2(t) and cp1d(t), were isolated from biological soil crusts (bscs) collected in the colorado plateau, usa. both strains were pigmented, gram-negative, non-motile rods and produced abundant mucus. they contained c(16 : 0), c(18 : 1)omega7c and c(14 : 0) 2-oh as the predominant cellular fatty acids, ubiquinone-10 as the isoprenoid quinone and sphingoglycolipid. based on the above characteristics, the isolates were assigned to the family sphingomonadaceae; 16 rrna gene ... | 2007 | 17473253 |
| papaya shoot tip associated endophytic bacteria isolated from in vitro cultures and host-endophyte interaction in vitro and in vivo. | fourteen distinct bacterial clones were isolated from surface-sterilized shoot tips (approximately 1 cm) of papaya (carica papaya l. 'surya') planted on murashige and skoog (ms)-based papaya culture medium (23/50 nos.) during the 2-4 week period following in vitro culturing. these isolates were ascribed to six gram-negative genera, namely pantoea (p. ananatis), enterobacter (e. cloacae), brevundimonas (b. aurantiaca), sphingomonas, methylobacterium (m. rhodesianum), and agrobacterium (a. tumefac ... | 2007 | 17538647 |
| investigation of microbial communities on reverse osmosis membranes used for process water production. | in the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (ro) membranes were determined. fresh surface water was used as a feed in a membrane-based water purification process. total dna was extracted from attached cells from feed spacer, ro membrane and product spacer. universal primers were used to amplify the bacterial 16s rrna genes. the biofilm community was analysed by 16s rrna-gene-targeted denaturing gradient gel electrophor ... | 2007 | 17546985 |
| sphingomonas pseudosanguinis sp. nov., isolated from the water reservoir of an air humidifier. | a yellow-pigmented bacterial isolate, strain g1-2(t), obtained from the surface of an air humidifier, was characterized taxonomically. 16s rrna gene sequence analysis, physiological characterization and estimation of the ubiquinone and polar lipid patterns and fatty acid composition revealed that strain g1-2(t) was similar to sphingomonas yabuuchiae and sphingomonas sanguinis, but also showed pronounced differences. on the basis of these results, a novel species of the genus sphingomonas is desc ... | 2007 | 17551055 |
| enhanced degradation of benzo[a]pyrene by mycobacterium sp. in conjunction with green alga. | previous work in this laboratory has confirmed that the bacteria mycobacterium sp. strain rjgii.135 and sphingomonas yanoikuyae strain b1 and the green alga selanastrum capricornutum strain utex 1648 degrade benzo[a]pyrene (bap) to various bap intermediates. s. capricornutum was first grown with bap for 4 days. the organic extract of this media was then introduced into separate cultures of strain rjgii.135 and strain b1; separate cultures were grown with bap for comparison. cultures grown with b ... | 2007 | 17555789 |
| molecular characterization of membrane-associated soluble serine palmitoyltransferases from sphingobacterium multivorum and bdellovibrio stolpii. | serine palmitoyltransferase (spt) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a (coa) to form 3-ketodihydrosphingosine (kds). eukaryotic spts comprise tightly membrane-associated heterodimers belonging to the pyridoxal 5'-phosphate (plp)-dependent alpha-oxamine synthase family. sphingomonas paucimobilis, a sphingolipid-containing bacterium, contains an abundant water-soluble homodimeric spt of the same family (h. ... | 2007 | 17557831 |
| degradation pathway of bisphenol a: does ipso substitution apply to phenols containing a quaternary alpha-carbon structure in the para position? | the degradation of bisphenol a and nonylphenol involves the unusual rearrangement of stable carbon-carbon bonds. some nonylphenol isomers and bisphenol a possess a quaternary alpha-carbon atom as a common structural feature. the degradation of nonylphenol in sphingomonas sp. strain ttnp3 occurs via a type ii ipso substitution with the presence of a quaternary alpha-carbon as a prerequisite. we report here a new degradation pathway of bisphenol a. consequent to the hydroxylation at position c-4, ... | 2007 | 17557840 |
| the structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. | sphingolipid biosynthesis commences with the condensation of l-serine and palmitoyl-coa to produce 3-ketodihydrosphingosine (kds). this reaction is catalysed by the plp-dependent enzyme serine palmitoyltransferase (spt; ec 2.3.1.50), which is a membrane-bound heterodimer (spt1/spt2) in eukaryotes such as humans and yeast and a cytoplasmic homodimer in the gram-negative bacterium sphingomonas paucimobilis. unusually, the outer membrane of s. paucimobilis contains glycosphingolipid (gsl) instead o ... | 2007 | 17559874 |
| a novel pathway for the biodegradation of gamma-hexachlorocyclohexane by a xanthomonas sp. strain ich12. | to isolate gamma-hexachlorocyclohexane (hch)-degrading bacteria from contaminated soil and characterize the metabolites formed and the genes involved in the degradation pathway. | 2007 | 17578411 |
| parameters controlling the gene-targeting frequency at the sphingomonas species rrn site and expression of the methyl parathion hydrolase gene. | to investigate the key parameters controlling the exogenous methyl parathion hydrolase (mph) gene mpd-targeting frequency at the ribosomal rna operon (rrn) site of sphingomonas species which has a wide range of biotechnological applications. | 2007 | 17578423 |
| bacterial synthesis of poly(hydroxybutyrate- co-hydroxyvalerate) using carbohydrate-rich mahua (madhuca sp.) flowers. | the objective of the present work was to utilize an unrefined natural substrate namely mahua (madhuca sp.) flowers, as a carbon source for the production of bacterial polyhydroxyalkanoate (pha) copolymer by bacillus sp-256. | 2007 | 17584466 |
| bacterial community composition and structure of biofilms developing on nanofiltration membranes applied to wastewater treatment. | the structure and microbial communities of biofilms developing on cross-flow nanofiltration (nf) membranes at different temperatures (20, 25 or 34 degrees c) and operation lengths (8h-24days) were studied. feedwater comprised tertiary quality wastewater effluent or synthetic media mimicking effluents of intermediate quality. after each run, the membranes were autopsied for bacterial enumeration, bacterial community composition and microscopy visualization (sem, clsm and afm/nsom). community comp ... | 2007 | 17585989 |
| sphingomonas astaxanthinifaciens sp. nov., a novel astaxanthin-producing bacterium of the family sphingomonadaceae isolated from misasa, tottori, japan. | a red-pigmented, gram-negative, motile, strictly aerobic, mesophilic, oval- or short rod-shaped bacterium (tdma-17(t)) was isolated from fresh water collected at misasa, a radioactive site in japan. tdma-17(t) was slightly tolerant against gamma-ray irradiation, and effectively produced carotenoids (2.8 mg g(-1) dry cells) including, astaxanthin and astaxanthin isomers. phylogenetic analysis based on 16s rrna gene sequences placed tdma-17(t) in a distinct lineage in the family sphingomonadaceae, ... | 2007 | 17590230 |
| novel aspects of symbiotic (polyvinyl alcohol) biodegradation. | a new polyvinyl alcohol (pva)-degrading bacterium was isolated from activated sludge sampled during a waste water treatment process and identified as sphingomonas sp. its pva oxidase activity and alcohol dehydrogenase activity for various low-molecular-weight secondary alcohols were detected. both activities were associated with cells of the degrader, and they were not extracellular. under optimal conditions, the isolate was able to degrade 500 mg of pva per litre in 2 weeks. the strain required ... | 2007 | 17594087 |
| diethyl phthalate in compost: ecotoxicological effects and response of the microbial community. | there is a great need to understand the environmental impacts of organic pollutants on soil health. phthalates are widely used in consumables and can be found extensively. we studied the toxicity of diethyl phthalate (dep), spiked in a compost plant growth substrate, by means of the acute toxicity flash test and on the basis of the germination and plant growth of radish seedlings. the response of the microbial community to dep in the growth substrate was studied by pcr-dgge (denaturing gradient ... | 2007 | 17258270 |
| dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment. | the structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. a laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with cu(ii) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. between 73 and 90 % of the cu(ii) was removed from water during long-term operation (over 200 days). ... | 2007 | 17259604 |
| sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity. | an aerobic, gram-negative, yellow-pigmented, non-motile bacterium, designated strain kmm 3882t, was isolated from a marine bivalve (anadara broughtoni) collected from peter the great bay, sea of japan, and was subjected to phenotypic and phylogenetic analyses. strain kmm 3882t was found to exert a remarkable inhibitory activity against a number of gram-positive micro-organisms. phylogenetic analysis based on 16s rrna gene sequences placed strain kmm 3882t within the genus sphingomonas, as an ind ... | 2007 | 17267979 |
| design of sphingomonad-detecting probes for a dna array, and its application to investigate the behavior, distribution, and source of rhizospherous sphingomonas and other sphingomonads inhabiting an acid sulfate soil paddock in kalimantan, indonesia. | throughout central and south kalimantan, indonesia, strongly acidic soil (ph 2.1-3.7) is widely distributed, and the local acidic soil-tolerant plants, including local rice varieties, often possess sphingomonads in their rhizosphere and rhizoplane. to investigate the behavior of sphingomonads inhabiting the rhizosphere of such acid-tolerant plants, we designed 13 different dna array probes (each of 72 mer) specific to a group of sphingomonads, using a hypervariable v6 region of the 16s rrna gene ... | 2007 | 17284854 |
| optimisation of the long-term efficacy of dental chair waterline disinfection by the identification and rectification of factors associated with waterline disinfection failure. | although many studies have highlighted the problem of biofilm growth in dental chair unit waterlines (duws), no long-term studies on the efficacy of duw disinfection using a large number of dental chair units (dcus) have been reported. | 2007 | 17303302 |
| isolation of a chlorpyrifos-degrading bacterium, sphingomonas sp. strain dsp-2, and cloning of the mpd gene. | a highly effective chlorpyrifos-degrading bacterium strain dsp-2 was isolated from the polluted treatment system of a chlorpyrifos manufacturer. this strain was preliminarily identified as sphingomonas sp. based on its morphological, physiological and biochemical tests as well as 16s rdna analysis. it utilized chlorpyrifos as its sole source of carbon for growth, by hydrolyzing chlorpyrifos to 3,5,6-trichloro-2-pyridinol (tcp). it could also utilize parathion, parathion-methyl, fenitrothion and ... | 2007 | 17306510 |
| 17beta-estradiol-degrading bacteria isolated from activated sludge. | fourteen phylogenetically diverse 17beta-estradiol-degrading bacteria (strains kc1-14) were isolated from activated sludge of a wastewater treatment plant. these isolates widely distributed among eight different genera--aminobacter (strains kc6 and kc7), brevundimonas (strain kc12), escherichia (strain kc13), flavobacterium (strain kc1), microbacterium (strain kc5), nocardioides (strain kc3), rhodococcus (strain kc4), and sphingomonas (strains kc8-kc11 and kc14)--of three phyla: proteobacteria, ... | 2007 | 17310711 |
| plant carbohydrate scavenging through tonb-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. | tonb-dependent receptors (tbdrs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in gram-negative bacteria. analysis of the genome of the phytopathogenic bacterium xanthomonas campestris pv. campestris (xcc), predicts 72 tbdrs. such an overrepresentation is common in xanthomonas species but is limited to only a small number of bacteria. here, we show that one xcc tbdr transports sucrose with a very high affinity, suggesting that it might be a sucro ... | 2007 | 17311090 |
| molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at vostok, east antarctica. | decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. at the vostok drill site, a total of 3650 m of ice core have now been obtained from the east antarctic ice sheet. the ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. in the present study we used 16s rrna gene sequencing to analyze the bacterial content of the vostok drilling fluid samp ... | 2007 | 17313578 |
| decolorisation and detoxification of direct blue-15 by a bacterial consortium. | studies were carried out on decolorisation and biotransformation of the dye direct blue-15 into 3,3'-dimethoxybenzidine (o'-dianisidine) and a sulphonated derivative by a five-member bacterial consortium. chromatographic studies revealed further complete biodegradation of 3,3'-dimethoxybenzidine coupled with release of ammonia, but the recalcitrant sulphonated derivative persisted. the microorganisms identified in the mixed consortium by 16s rdna sequence analysis were alcaligenes faecalis, sphi ... | 2007 | 17321737 |
| microorganisms isolated from the water phase of tropospheric clouds at the puy de dôme: major groups and growth abilities at low temperatures. | this work constitutes the first large report on aerobic cultivable microorganisms present in cloud water. seven cloud-event samples were collected at the puy de dôme summit, and cultivation was performed leading to the isolation of 71 bacterial, 42 fungal and 15 yeast strains. most of the fungi isolated were of cladosporium or trametes affiliation, and yeasts were of cryptococcus affiliation. bacteria, identified on the basis of their 16s rrna gene sequence, were found to belong to actinobacteri ... | 2007 | 17328765 |
| cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading sphingomonas sp. strain. | a carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. the isolate, designated sphingomonas sp. strain xldn2-5, could utilize carbazole (ca) as the sole source of carbon, nitrogen, and energy. washed cells of strain xldn2-5 were shown to be capable of degrading dibenzofuran (dbf) and dibenzothiophene (dbt). examination of metabolites suggested that xldn2-5 degraded dbf to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic a ... | 2007 | 17337542 |
| structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1. | the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ... | 2007 | 17349044 |
| integrated response to inducers by communication between a catabolic pathway and its regulatory system. | efficient gene regulation of metabolic pathways implies that the profile of molecules inducing the pathway matches that of the molecules that are metabolized. gratuitous induction, a well-known phenomenon in catabolic pathways, is the consequence of differences in the substrate and inducer profiles. this phenomenon is particularly evident in pathways for biodegradation of organic contaminants that can be induced by a variety of molecules similar to the real substrates. analysis of the regulation ... | 2007 | 17351041 |
| effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. | to date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. however, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. in this study, we characterized a collection of 61 bacterial strains isolated from scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. the ability of bacteria to weather bi ... | 2007 | 17351101 |
| culturable leaf-associated bacteria on tomato plants and their potential as biological control agents. | culturable leaf-associated bacteria inhabiting a plant have been considered as promising biological control agent (bca) candidates because they can survive on the plant. we investigated the relationship between bacterial groups of culturable leaf-associated bacteria on greenhouse- and field-grown tomato leaves and their antifungal activities against tomato diseases in vitro and in vivo. in addition, the isolated bacteria were analyzed for n-acyl-homoserine lactone (ahl) and indole-3-acetic acid ... | 2007 | 17356949 |
| role of dissolved humic acids in the biodegradation of a single isomer of nonylphenol by sphingomonas sp. | this study shows the important role of humic acids in the degradation of (14)c and (13)c labeled isomer of np by sphingomonas sp. strain ttnp3 and the detoxification of the resulting metabolites. due to the association of np with humic acids, its solubility in the medium was enhanced and the extent of mineralization of nonylphenol increased from 20% to above 35%. this was accompanied by the formation of significant amounts of np residues bound to the humic acids, which also occurred via abiotic ... | 2007 | 17367841 |
| elucidation of the ipso-substitution mechanism for side-chain cleavage of alpha-quaternary 4-nonylphenols and 4-t-butoxyphenol in sphingobium xenophagum bayram. | recently we showed that degradation of several nonylphenol isomers with alpha-quaternary carbon atoms is initiated by ipso-hydroxylation in sphingobium xenophagum bayram (f. l. p. gabriel, a. heidlberger, d. rentsch, w. giger, k. guenther, and h.-p. e. kohler, j. biol. chem. 280:15526-15533, 2005). here, we demonstrate with 18o-labeling experiments that the ipso-hydroxy group was derived from molecular oxygen and that, in the major pathway for cleavage of the alkyl moiety, the resulting nonanol ... | 2007 | 17369338 |
| the recent evolution of pentachlorophenol (pcp)-4-monooxygenase (pcpb) and associated pathways for bacterial degradation of pcp. | man-made polychlorinated phenols such as pentachlorophenol (pcp) have been used extensively since the 1920s as preservatives to prevent fungal attack on wood. during this time, they have become serious environmental contaminants. despite the recent introduction of pcp in the environment on an evolutionary time scale, pcp-degrading bacteria are present in soils worldwide. the initial enzyme in the pcp catabolic pathway of numerous sphingomonads, pcp-4-monooxygenase (pcpb), catalyzes the para-hydr ... | 2007 | 17123025 |
| the catalytic pocket of the ring-hydroxylating dioxygenase from sphingomonas chy-1. | ring-hydroxylating dioxygenases are multicomponent bacterial enzymes that catalyze the first step in the oxidative degradation of aromatic hydrocarbons. the dioxygenase from sphingomonas chy-1 is unique in that it can oxidize a wide range of polycyclic aromatic hydrocarbons (pahs). with a crystal structure similar to that of the seven other known dioxygenases, its catalytic domain features the largest hydrophobic substrate binding cavity characterized so far. molecular modeling studies indicated ... | 2007 | 17157819 |
| the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole. | we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ... | 2007 | 17172338 |
| genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. | lignins are the most abundant aromatic compounds in nature, and their decomposition is essential to the terrestrial carbon cycle. white rot fungi secreting phenol oxidases are assumed to be involved in the initial degradation of native lignin, whereas bacteria play a main role in the mineralization of lignin-derived low-molecular-weight compounds in soil. there are a number of reports on the degradation pathways for lignin-derived aromatic compounds, but their catabolism has not been enzymatical ... | 2007 | 17213657 |
| biodegradation of bisphenol a and related compounds by sphingomonas sp. strain bp-7 isolated from seawater. | a bacterium capable of assimilating 2,2-bis(4-hydroxyphenyl)propane (bisphenol a), strain bp-7, was isolated from offshore seawater samples on a medium containing bisphenol a as sole source of carbon and energy, and identified as sphingomonas sp. strain bp-7. other strains, pseudomonas sp. strain bp-14, pseudomonas sp. strain bp-15, and strain no. 24a, were also isolated from bisphenol a-enrichment culture of the seawater. these strains did not degrade bisphenol a, but accelerated the degradatio ... | 2007 | 17213659 |
| influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by sphingomonas sp. strain pheb4. | the influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (pahs) was investigated when sphingomonas sp. strain pheb4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (pmsm) or nutrient broth (nb). the nb-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate pahs compared to the pmsm-grown culture. the concentrations of pah metabolites were also lower in nb- ... | 2007 | 17216444 |
| description of sphingosinicella xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus sphingosinicella and the species sphingosinicella microcystinivorans. | a gram-negative, rod-shaped bacterium, strain 3-2w4(t), was isolated from the aeration tank of a wastewater treatment plant in zurich and was found to have the exceptional capacity to degrade synthetic beta-peptides. 16s rrna gene sequence analysis showed that strain 3-2w4(t) is closely related to sphingosinicella microcystinivorans y2(t), but dna-dna hybridization experiments between these two strains revealed that they belong to two different species. the two strains displayed different finger ... | 2007 | 17220451 |
| changes to the structure of sphingomonas spp. communities associated with biodegradation of the herbicide isoproturon in soil. | the phenyl-urea herbicide isoproturon is a major contaminant of surface and ground-water in agricultural catchments. earlier work suggested that within-field spatial variation of isoproturon degradation rate resulted from interactions between catabolizing sphingomonas spp. and ph. in the current study, changes to the structure of sphingomonas communities during isoproturon catabolism were investigated using sphingomonas-specific 16s rrna gene primers. growth-linked catabolism at high-ph (>7.5) s ... | 2007 | 17241244 |
| measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions. | substrate depletion experiments were conducted to characterize aerobic biodegradation of 20 single polycyclic aromatic hydrocarbons (pahs) by induced sphingomonas paucimobilis strain epa505 in liquid suspensions. pahs consisted of low molecular weight, unsubstituted, and methyl-substituted homologs. a material balance equation containing the andrews kinetic model, an extension of the monod model accounting for substrate inhibition, was numerically fitted to batch depletion data to estimate extan ... | 2007 | 17115446 |
| kinetics of biodegradation of binary and ternary mixtures of pahs. | the kinetics of biodegradation of mixtures of polycyclic aromatic hydrocarbons (pahs) by sphingomonas paucimobilis strain epa505 were investigated. the investigation focused on three- and four-ring pahs, specifically 2-methylphenanthrene, fluoranthene, and pyrene. uptake rates in aerobic batch suspended cultivations were measured for the individual pahs and their binary and ternary mixtures. it was observed that kinetics were influenced by the mixture composition and the kinetic properties of th ... | 2007 | 17115447 |